SAXSdb — 1avv

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

NEGATIVE FACTOR

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 58–206	Fragment：CORE DOMAIN Mutation：DEL(2-57), N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 3.00 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1AVV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVZ V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN Deposited 1997-09-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 58–206（149 aa） Fragment：CONSERVED CORE DOMAIN Chain B 58–206（149 aa） Fragment：CONSERVED CORE DOMAIN	Mutation：N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE) Mutation：N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.9；pH 8.9	Resolution 3.00 Å R-free 0.270
1EFN HIV-1 NEF PROTEIN IN COMPLEX WITH R96I MUTANT FYN SH3 DOMAIN Deposited 1996-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 54–205（152 aa） Fragment：CONSERVED CORE DOMAIN OF NEF, RESIDUES 71-203 Chain D 54–205（152 aa） Fragment：CONSERVED CORE DOMAIN OF NEF, RESIDUES 71-203	Mutation：T71R Mutation：T71R	PBM TRIMETHYL LEAD ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.282
4D8D Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant Deposited 2012-01-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 58–204（147 aa） Fragment：CONSERVED CORE DOMAIN (UNP Residues 58-204)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；0.3 M sodium potassium tartrate, 0.5 M bicine buffer , 1cmc D-octylglucopyranoside, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.52 Å R-free 0.238
4D8D Crystal structure of HIV-1 NEF Fyn-SH3 R96W variant Deposited 2012-01-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 58–204（147 aa） Fragment：CONSERVED CORE DOMAIN (UNP Residues 58-204)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；0.3 M sodium potassium tartrate, 0.5 M bicine buffer , 1cmc D-octylglucopyranoside, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.52 Å R-free 0.238

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEF_HV1BR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–151； UniProt 58–206

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1avv
Deposition date deposition_date	1997-09-21
Structure title title	HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN
Keywords keywords	MYRISTYLATION, GTP-BINDING, PHOSPHORYLATION, HIV-1, NEF, VIRUS, PXXP MOTIF; MYRISTYLATION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	14.28 Å
Radius of gyration Rg (electron density) rg_electron	13.06 Å
Forward intensity I(0) i0	2673610.00
Molecular weight molecular_weight	11830.0 kDa
Excluded volume excluded_volume	15004 Å³
Envelope volume envelope_volume	16388 Å³
Hydration-shell volume shell_volume	10771 Å³
Envelope diameter envelope_diameter	43.6 Å
Shell Rg shell_rg	18.64 Å
Envelope Rg envelope_rg	13.38 Å
Shape Rg shape_rg	13.03 Å
Total Rg total_rg	14.46 Å
Total atoms total_atoms	843
Residues n_residues	99
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	45.0 Å
Rg (real space) rg_real	14.18 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	2.6740e+06
I(0) uncertainty (real space) i0_real_error	2.6020e+04
Rg (reciprocal space) rg_reciprocal	14.18 Å
I(0) (reciprocal space) i0_reciprocal	2674000.0000
Solution quality estimate total_estimate	0.8964
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.2 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.386
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	419700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1avva_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.102 — Regulatory factor Nef
Superfamily Superfamily superfamily	d.102.1 — Regulatory factor Nef
Family Family family	d.102.1.1 — Regulatory factor Nef

CATH v4.4 (1 domains)

Domain ID domain_id	1avvA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

▶

8. Citations (3)

▶

Unit-cell length a length_a	85.160 Å
Unit-cell length b length_b	85.160 Å
Unit-cell length c length_c	85.160 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 2 3
Space-group number int_tables_number	195
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2800

Description description	NEGATIVE FACTOR
Molecular weight formula_weight	17568.7 kDa
Mutation mutation	DEL(2-57), N-TERMINAL RESIDUES GS (PART OF A THROMBIN CLEAVAGE SITE)
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	843

HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN

1. Protein Identity and Related Structures Protein Identity & Related Structures

NEGATIVE FACTOR

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/av/1avv/1avv.fit
pddf	/app/data/pr_computation/av/1avv/1avv.pr.out
profile	/app/data/saxs_computation/av/1avv/1avv.dat